Let's all take a step back and take a deep breath...
It's about time OP shared a little more info with us. As it stands, we're all shooting at noises in the night.
It would be nice if OP told us exactly which make and model Onkyo he's running and, while we're at it, the make and model of the subwoofer involved also.
Perhaps then some logical suggestions can be made. As it now stands, we're sniping each other and he's having a grand old time just sitting back watching the show.
Until then, I recommend a moratorium on this thread.
OK, I found on another thread where he listed his equipment. Here's what's up:
1) The receiver is a straight stereo unit. No subwoofer output. Not even a line level output. His only option to connect a subwoofer is via speaker level outputs and use the sub's crossover as a low-pass filter, which is what it seems he's done aready.
2) The sub has both line level and speaker level inputs. No outputs are offered for either so he must run the speakers full range. As mentioned above, line level is not an option so he's got it hooked up about as well as he can.
Unfortunately, the sub's lack of high pass filtering doesn't allow him to avail himself of the option of preventing lows from getting to his mains.
I would suggest he connect both the sub and the mains to the same speaker terminals in case speakers "A" and "B" are connected in series when they are both selected.
He can kerfutz with the low-pass filter and level controls on the sub but that's about all. If he can't arrive at a workable sound then, it's either the source, the speakers, or his expectations. My $$ is on either the former or the latter.